rs9904838

Variant names:

• chr17-55968960-A-G
• rs9904838
• ENST00000653862.1:c.208+3284A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653862.1(ANKFN1):​c.208+3284A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 151,928 control chromosomes in the GnomAD database, including 2,386 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.13 (2386 hom., cov: 31)
• Consequence: ANKFN1 ENST00000653862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 3 publications found

Genes affected

ANKFN1 (HGNC:26766): (ankyrin repeat and fibronectin type III domain containing 1) Predicted to be involved in establishment of mitotic spindle orientation and regulation of establishment of bipolar cell polarity. Predicted to act upstream of or within behavioral fear response; equilibrioception; and locomotor rhythm. Predicted to be active in spindle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKFN1	ENST00000653862.1	c.208+3284A>G		intron_variant	Intron 2 of 21			ENSP00000499705.1
ANKFN1	ENST00000635860.2	c.34+3284A>G		intron_variant	Intron 3 of 22	5		ENSP00000489811.2

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19101 AN: 151810 Hom.: 2358 Cov.: 31

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.0341

Gnomad AMR AF: 0.0763

Gnomad ASJ AF: 0.0695

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.0269

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0375

Gnomad OTH AF: 0.111

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.126 AC: 19175 AN: 151928 Hom.: 2386 Cov.: 31 AF XY: 0.126 AC XY: 9340 AN XY: 74260

African (AFR) AF: 0.321 AC: 13254 AN: 41334

American (AMR) AF: 0.0762 AC: 1163 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0695 AC: 241 AN: 3468

East Asian (EAS) AF: 0.103 AC: 531 AN: 5166

South Asian (SAS) AF: 0.174 AC: 835 AN: 4812

European-Finnish (FIN) AF: 0.0269 AC: 285 AN: 10592

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0375 AC: 2552 AN: 67976

Other (OTH) AF: 0.117 AC: 247 AN: 2110

Alfa AF: 0.0669 Hom.: 3068

Bravo AF: 0.136

Asia WGS AF: 0.170 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.029
DANN	Benign	0.35
PhyloP100		-2.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9904838; hg19: chr17-54046321;